Hi Marina,The issue was resolved during further discussion in email.The problem was with different set of filters in VS and in command line.

There are few more possible reasons for such symptoms:- different versions of source code are being analyzed- assemblies are built with different build settings (e.g. with or without compiler optimizations)- issue with getting per-test information for child processes from the VS (http://youtrack.jetbrains.com/issue/DCVR-6819)(fixed and will be included into dotCover 3.0, there are workarounds for previous versions)